One of the most complex challenges of heritage sciences is the identification and protection of buried archaeological heritage in urban areas and the need to manage, maintain and inspect underground services. Archaeology and geophysics, used in an integrated way, provide an important contribution to open new perspectives in understanding both the history of cities and in helping the decision makers in planning and governing the urban development and management. The problems of identification and interpretation of geophysical features in urban subsoil make it necessary to develop ad hoc procedures to be implemented and validated in significant case studies. This paper deals with the results of an interdisciplinary project in Cusco (Peru), the capital of Inca Empire, where the georadar method was applied for the first time in the main square. The georadar method was successfully employed based on knowledge of the historical evolution of Cusco and the availability of archaeological records provided by some excavations nearby the study area. Starting from a model for the electromagnetic wave reflection from archaeological structures and pipes, georadar results were interpreted by means of comparative morphological analysis of high amplitude values observed from time slices with reflectors visualized in the radargrams.